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exiting after errors in guidance.py

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Auden Cote-L'Heureux 2024-02-07 11:30:26 -05:00 committed by GitHub
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commit 0f2ae76d13
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1 changed files with 4 additions and 2 deletions
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PTL2/Scripts/guidance.py
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@ -12,10 +12,12 @@ def run(params):
if not os.path.isdir(preguidance_path): if not os.path.isdir(preguidance_path):
print('\nERROR: The path ' + preguidance_path + ' could not be found when trying to locate pre-Guidance (unaligned) files. Make sure that the --start and --data parameters are correct and/or that the pre-Guidance step ran successfully.\n') print('\nERROR: The path ' + preguidance_path + ' could not be found when trying to locate pre-Guidance (unaligned) files. Make sure that the --start and --data parameters are correct and/or that the pre-Guidance step ran successfully.\n')
exit()
if len([f for f in os.listdir(preguidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]) == 0: if len([f for f in os.listdir(preguidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]) == 0:
print('\nERROR: No pre-Guidance (unaligned) files could be found at the path ' + preguidance_path + '. Make sure that the --start and --data parameters are correct, that the pre-Guidance step ran successfully, and that the unaligned files are formatted correctly (they must have the file extension .faa, .fa, or .fasta).\n') print('\nERROR: No pre-Guidance (unaligned) files could be found at the path ' + preguidance_path + '. Make sure that the --start and --data parameters are correct, that the pre-Guidance step ran successfully, and that the unaligned files are formatted correctly (they must have the file extension .faa, .fa, or .fasta).\n')
exit()
os.mkdir(params.output + '/Output/Intermediate/Guidance') os.mkdir(params.output + '/Output/Intermediate/Guidance')
os.mkdir(params.output + '/Output/Intermediate/Guidance/Input') os.mkdir(params.output + '/Output/Intermediate/Guidance/Input')
os.mkdir(params.output + '/Output/Intermediate/Guidance/Output') os.mkdir(params.output + '/Output/Intermediate/Guidance/Output')